The phylogeographic relationships of the trans-Palearctic Willow Tit assemblage were studied by obtaining sequence data from the mitochondrial cytochrome b gene from 34 specimens representing nine subspecies from across the species range. Four distinct genetic groups were identified: Parus montanus weigoldicus, P. m. affinis, P. m. songarus, and a clade containing six Eurasian subspecies (ssp. baicalensis, borealis, montanus, restrictus, rhenanus, and sachalinensis). P. m. weigoldicus, P. m. affinis, and P. m. songarus were reciprocally monophyletic and separated from each other and other subspecies by uncorrected genetic distances between 1.9 and 5.8%. The remaining six subspecies were closely related and shared mitochondrial haplotypes, despite marked morphological and acoustical differences, suggesting a rapid evolution of distinct vocalization patterns. The current classification splitting the species into the songarus and montanus subspecies groups is not concordant with our phylogeny. Also, the four regiolect groups, Lowland, Alpine, Siberian, and Sino-Japanese, are not fully mirrored in the phylogeny. Our data suggest that the mono-frequency song type may be ancestral and was retained over a long evolutionary time in certain populations, but was altered or camouflaged by learning processes in others.